Experiment: 7XVN

Structural basis for DNA recognition feature of retinoid-related orphan receptors

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6L6L	6L6L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	291	0.1 M MES pH 5.6, 0.1 M (NH4)2SO4, 0.01 M MgCl2, 22% PEG 8K

Crystal Properties
Matthews coefficient	Solvent content
1.67	26.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.627	α = 90
b = 64.584	β = 90
c = 238.635	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 S 9M		2021-12-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL10U2	0.97918	SSRF	BL10U2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.302	32	99	0.1416	0.995	11.33	7.1		43676

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.302	2.384			0.683

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6L6L	2.302	32	1.33	43676	3668	98.16	0.2117	0.2078	0.2123	0.2559	0.258	54.9235

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	22.902
f_angle_d	0.672
f_chiral_restr	0.043
f_bond_d	0.007
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2270
Nucleic Acid Atoms	1476
Solvent Atoms	119
Heterogen Atoms	8

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing